Recent Research Examining Links Among Klebsiella pneumoniae from Food, Food Animals, and Human Extraintestinal Infections

Extended-Spectrum Beta-Lactamase-Producing Escherichia coli and Other Antimicrobial-Resistant Gram-Negative Pathogens Isolated from Bovine Mastitis: A One Health Perspective

Antimicrobial resistance (AMR) poses an imminent threat to global public health, driven in part by the widespread use of antimicrobials in both humans and animals. Within the dairy cattle industry, Gram-negative coliforms such as Escherichia coli and Klebsiella pneumoniae stand out as major causative agents of clinical mastitis. These same bacterial species are frequently associated with severe infections in humans, including bloodstream and urinary tract infections, and contribute significantly to the alarming surge in antimicrobial-resistant bacterial infections worldwide. Additionally, mastitis-causing coliforms often carry AMR genes akin to those found in hospital-acquired strains, notably the extended-spectrum beta-lactamase genes. This raises concerns regarding the potential transmission of resistant bacteria and AMR from mastitis cases in dairy cattle to humans. In this narrative review, we explore the distinctive characteristics of antimicrobial-resistant E. coli and Klebsiella spp. strains implicated in clinical mastitis and human infections. We focus on the molecular mechanisms underlying AMR in these bacterial populations and critically evaluate the potential for interspecies transmission. Despite some degree of similarity observed in sequence types and mobile genetic elements between strains found in humans and cows, the existing literature does not provide conclusive evidence to assert that coliforms responsible for mastitis in cows pose a direct threat to human health. Finally, we also scrutinize the existing literature, identifying gaps and limitations, and propose avenues for future research to address these pressing challenges comprehensively.

Susceptible bacteria can survive antibiotic treatment in the mammalian gastrointestinal tract without evolving resistance

Antibiotic resistance and evasion are incompletely understood and complicated by the fact that murine interval dosing models do not fully recapitulate antibiotic pharmacokinetics in humans. To better understand how gastrointestinal bacteria respond to antibiotics, we colonized germ-free mice with a pan-susceptible genetically barcoded Escherichia coli clinical isolate and administered the antibiotic cefepime via programmable subcutaneous pumps, allowing closer emulation of human parenteral antibiotic dynamics. E. coli was only recovered from intestinal tissue, where cefepime concentrations were still inhibitory. Strikingly, "some" E. coli isolates were not cefepime resistant but acquired mutations in genes involved in polysaccharide capsular synthesis increasing their invasion and survival within human intestinal cells. Deleting wbaP involved in capsular polysaccharide synthesis mimicked this phenotype, allowing increased invasion of colonocytes where cefepime concentrations were reduced. Additionally, "some" mutant strains exhibited a persister phenotype upon further cefepime exposure. This work uncovers a mechanism allowing "select" gastrointestinal bacteria to evade antibiotic treatment.

Contribution of Food to the Human Health Burden of Antimicrobial Resistance

The impact of foodborne antimicrobial resistance (AMR) on the human health burden of AMR infections is unknown. The aim of this review was to evaluate and summarize the scientific literature investigating all potential sources of human AMR infections related to food. A literature search was conducted in Embase (Ovid) and MEDLINE (Ovid) databases to identify appropriate studies published between 2010 and 2023. The results of the search were reviewed and categorized based on the primary subject matter. Key concepts from each category are described from the perspective of food safety as a public health objective. The search yielded 3457 references, 1921 remained after removal of duplicates, abstracts, editorials, comments, notes, retractions, and errata. No properly designed source attribution studies were identified, but 383 journal articles were considered relevant and were classified into eight subcategories and discussed in the context of four streams of evidence: prevalence data, epidemiological studies, outbreak investigations and human health impact estimates. There was sufficient evidence to conclude that AMR genes, whether present in pathogenic or nonpathogenic bacteria, constitute a foodborne hazard. The level of consumer risk owing to this hazard cannot be accurately estimated based on the data summarized here. Key gaps in the literature are noted.

Prevalence and antimicrobial resistance profiles of extended-spectrum beta-lactamase-producing Escherichia coli in East Tennessee dairy farms

Introduction

The extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, such as Escherichia coli, are emerging as a serious threat to global health due to their rapid spread and their multidrug-resistant (MDR) phenotypes. However, limited information is available regarding the prevalence and antimicrobial resistance (AMR) profile of ESBL-E. coli in the United States dairy farms. This study aimed to determine the prevalence and AMR pattern of ESBL-E. coli in East Tennessee dairy cattle farms.

Methods

Rectal fecal samples from dairy cattle (n = 508) and manure (n = 30), water (n = 19), and feed samples (n = 15) were collected from 14 farms. The presumptive E. coli was isolated on CHROMagar™ ESBL and confirmed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). Antimicrobial susceptibility testing was performed on the ESBL-E. coli isolates.

Results and discussion

From 572 fecal and farm environmental samples, a total of 233 (41%, n = 572) ESBL-E. coli were identified. The prevalence of fecal ESBL-E. coli was 47.5% (95% CI: 46.2-49.2). The within-farm prevalence of ESBL-E. coli ranged from 8 to 100%. Recent treatment history with third-generation cephalosporins (3GC), cow parity ≥3, and calves were the independent risk factors associated (P < 0.05) with fecal carriage of ESBL-E. coli. Overall, 99.6% (n = 231) ESBL-E. coli tested were phenotypically resistant to at least one of the 14 antimicrobial agents tested. The most common AMR phenotypes were against beta-lactam antibiotics, ampicillin (99.1%; n = 231 isolates), and ceftriaxone (98.7%, n = 231). Most ESBL-E. coli isolates (94.4%) were MDR (resistance to ≥3 antimicrobial classes), of which 42.6% showed co-resistance to at least six classes of antimicrobials. ESBL-E. coli isolates with concurrent resistance to ceftriaxone, ampicillin, streptomycin, tetracycline, sulfisoxazole, and chloramphenicol are widespread and detected in all the farms. The detection of MDR ESBL-E. coli suggests that dairy cattle can be a reservoir for these bacteria, highlighting the associated public health risk.

Characterization of color, metabolites and microbial community dynamics of doubanjiang during constant temperature fermentation

This study aimed to elaborate the effect of temperature on doubanjiang fermentation. Two batches of constant-temperature groups were prepared and their physicochemical parameters, color formation, metabolites and microbial community dynamics during fermentation were determined and compared with those of natural temperature fermentation group. The results showed that fermentation at 40 °C could accelerate the accumulation of amino nitrogen, reducing sugar, amino acids, organic acids and various volatile metabolites while it was able to inhibit the growth of conditionally pathogenic bacteria, such as Klebsiella and Salmonella. However, high concentrations of total acids and biogenic amines, protrusive burnt flavor and darker color were observed in constant temperature fermentation, which were unfavorable for doubanjiang quality. Higher fermentation temperature lowered the diversity of bacterial community and favored the growth of Bacillus genus. The correlation between key microbial genera and doubanjiang quality indexes were significantly different among different temperatures. This study would deep our understanding of the roles of temperature ondoubanjiangfermentation.

Hypervirulent Klebsiella pneumoniae among diarrheic farm animals: A serious public health concern

Hypervirulent Klebsiella pneumoniae (hvKp) is an emerging pathogen and it has more virulence factors than classical Klebsiella pneumoniae strains. Carbapenem-resistant hvKp (CR-hvKp) is a dangerous bacteria that has both high virulence and antibiotic resistance and poses a global public health problem worldwide. The current study was carried out to investigate the occurrence of hvKp as well as carbapenem-resistant Klebsiella pneumoniae (CRKP) and CR-hvKp among diarrheic farm animals. For this purpose, rectal swabs from 165 farm animals (45 cattle, 66 sheep, and 54 goats) were collected. Samples were processed for the isolation and identification of Klebsiella pneumoniae. Moreover, hvKp was detected using molecular techniques by amplification of biomarker virulence genes (rmpA, rmpA2, iucA, iroB, and peg-344), followed by a string test. On the other hand, all K. pneumoniae isolates were examined for carbapenem resistance by both phenotypic and molecular methods. The phylogenetic analysis of peg-344 sequences was carried out. The overall prevalence rates of K. pneumoniae, hvKp, CRKP, and CR-hvKp were 24.2%, 7.9%, 16.4%, and 6.1% respectively. HvKp and CR-hvKp were detected among all examined farm animal species. On a Molecular basis, all biomarker virulence genes were identified except iroB, but rmpA is the most prevalent one. The phylogenetic analysis of peg-344 sequences obtained from the study points out their genetic relatedness to those circulated among humans. In conclusion, the emergence of hvKp and CR-hvKp among diarrheic farm animals confers a great public health implication and thus, the possible animal reservoirs for such hypervirulent-antimicrobial resistant strains cannot be ruled out.

From Farm to Fork: Persistence of Clinically Relevant Multidrug-Resistant and Copper-Tolerant Klebsiella pneumoniae Long after Colistin Withdrawal in Poultry Production

Concerns about colistin-resistant bacteria in animal food-environmental-human ecosystems prompted the poultry sector to implement colistin restrictions and explore alternative trace metals/copper feed supplementation. The impact of these strategies on the selection and persistence of colistin-resistant Klebsiella pneumoniae in the whole poultry production chain needs clarification. We assessed colistin-resistant and copper-tolerant K. pneumoniae occurrence in chickens raised with inorganic and organic copper formulas from 1-day-old chicks to meat (7 farms from 2019 to 2020), after long-term colistin withdrawal (>2 years). Clonal diversity and K. pneumoniae adaptive features were characterized by cultural, molecular, and whole-genome-sequencing (WGS) approaches. Most chicken flocks (75%) carried K. pneumoniae at early and preslaughter stages, with a significant decrease (P < 0.05) in meat batches (17%) and sporadic water/feed contamination. High rates (>50%) of colistin-resistant/mcr-negative K. pneumoniae were observed among fecal samples, independently of feed. Most samples carried multidrug-resistant (90%) and copper-tolerant (81%; silA and pcoD positive and with a MICCuSO4 of ≥16 mM) isolates. WGS revealed accumulation of colistin resistance-associated mutations and F type multireplicon plasmids carrying antibiotic resistance and metal/copper tolerance genes. The K. pneumoniae population was polyclonal, with various lineages dispersed throughout poultry production. ST15-KL19, ST15-KL146, and ST392-KL27 and IncF plasmids were similar to those from global human clinical isolates, suggesting chicken production as a reservoir/source of clinically relevant K. pneumoniae lineages and genes with potential risk to humans through food and/or environmental exposure. Despite the limited mcr spread due to the long-term colistin ban, this action was ineffective in controlling colistin-resistant/mcr-negative K. pneumoniae, regardless of feed. This study provides crucial insights into the persistence of clinically relevant K. pneumoniae in the poultry production chain and highlights the need for continued surveillance and proactive food safety actions within a One Health perspective. IMPORTANCE The spread of bacteria resistant to last-resort antibiotics such as colistin throughout the food chain is a serious concern for public health. The poultry sector has responded by restricting colistin use and exploring alternative trace metals/copper feed supplements. However, it is unclear how and to which extent these changes impact the selection and persistence of clinically relevant Klebsiella pneumoniae throughout the poultry chain. We found a high occurrence of copper-tolerant and colistin-resistant/mcr-negative K. pneumoniae in chicken flocks, regardless of inorganic and organic copper formulas use and a long-term colistin ban. Despite the high K. pneumoniae isolate diversity, the occurrence of identical lineages and plasmids across samples and/or clinical isolates suggests poultry as a potential source of human K. pneumoniae exposure. This study highlights the need for continued surveillance and proactive farm-to-fork actions to mitigate the risks to public health, relevant for stakeholders involved in the food industry and policymakers tasked with regulating food safety.

The Antibacterial Activity of Rhazya stricta Extracts against Klebsiella pneumoniae Isolated from Some Soil Invertebrates at High Altitudes

Klebsiella is a common dangerous pathogen for humans and animals and is widely present in the digestive system. The genus Klebsiella is ubiquitous, as it is endemic to surface water, soil, and sewage. In this study, 70 samples were obtained from soil-dwelling invertebrates from September 2021 to March 2022 from Taif and Shafa in different altitudinal regions of Saudi Arabia. Fifteen of these samples were identified as Klebsiella spp. The Klebsiella isolates were genetically identified as Klebsiella pneumoniae using rDNA sequencing. The antimicrobial susceptibility of the Klebsiella isolates was determined. Amplification of virulence genes was performed using PCR. In this study, 16S rDNA sequencing showed a similarity from 98% to 100% with related K. pneumonia from the NCBI database, and the sequences were deposited in the NCBI GenBank under accession numbers ON077036 to ON077050. The growth inhibition properties of ethanolic and methanolic extracts of the medicinal plant Rhazya stricta's leaves against K. pneumoniae strains using the minimum inhibitory concentration (MIC) method and disc diffusion were evaluated. In addition, the biofilm inhibitory potential of these extracts was investigated using crystal violet. HPLC analysis identified 19 components divided into 6 flavonoids, 11 phenolic acids, stilbene (resveratrol), and quinol, and revealed variations in the number of components and their quantities between extracts. Both extracts demonstrated interesting antibacterial properties against K. pneumoniae isolates. The 2 extracts also showed strong biofilm inhibitory activities, with percentages of inhibition extending from 81.5% to 98.7% and from 35.1% to 85.8% for the ethanolic and methanolic extracts, respectively. Rhazya stricta leaf extract revealed powerful antibacterial and antibiofilm activities against K. pneumoniae isolates and could be a good candidate for the treatment or prevention of K. pneumonia-related infections.

Cell membrane-coated nanoparticles: An emerging antibacterial platform for pathogens of food animals

Bacterial pathogens of animals impact food production and human health globally. Food animals act as the major host reservoirs for pathogenic bacteria and thus are highly prone to suffer from several endemic infections such as pneumonia, sepsis, mastitis, and diarrhea, imposing a major health and economical loss. Moreover, the consumption of food products of infected animals is the main route by which human beings are exposed to zoonotic bacteria. Thus, there is excessive and undue administration of antibiotics to fight these virulent causative agents of food-borne illness, leading to emergence of resistant strains. Thus, highprevalence antibiotic-resistant resistant food-borne bacterial infections motivated the researchers to discover new alternative therapeutic strategies to eradicate resistant bacterial strains. One of the successful therapeutic approach for the treatment of animal infections, is the application of cell membrane-coated nanoparticles. Cell membranes of several different types of cells including platelets, red blood cells, neutrophils, cancer cells, and bacteria are being wrapped over the nanoparticles to prepare biocompatible nanoformulations. This diversity of cell membrane selection and together with the possibility of combining with an extensive range of nanoparticles, has opened a new opportunistic window for the development of more potentially effective, safe, and immune evading nanoformulations, as compared to conventionally used bare nanoparticle. This article will elaborately discuss the discovery and development of novel bioinspired cell membrane-coated nanoformulations against several pathogenic bacteria of food animals such as Klebsiella pneumoniae, Escherichia coli, Staphylococcus aureus, Salmonella enteritidis, Campylobacter jejuni, Helicobacter pylori, and Group A Streptococcus and Group B Streptococcus.

Susceptible bacteria survive antibiotic treatment in the mammalian gastrointestinal tract without evolving resistance

In vitro systems have provided great insight into the mechanisms of antibiotic resistance. Yet, in vitro approaches cannot reflect the full complexity of what transpires within a host. As the mammalian gut is host to trillions of resident bacteria and thus a potential breeding ground for antibiotic resistance, we sought to better understand how gut bacteria respond to antibiotic treatment in vivo . Here, we colonized germ-free mice with a genetically barcoded antibiotic pan-susceptible Escherichia coli clinical isolate and then administered the antibiotic cefepime via programmable subcutaneous pumps which allowed for closer emulation of human parenteral antibiotic pharmacokinetics/dynamics. After seven days of antibiotics, we were unable to culture E. coli from feces. We were, however, able to recover barcoded E. coli from harvested gastrointestinal (GI) tissue, despite high GI tract and plasma cefepime concentrations. Strikingly, these E. coli isolates were not resistant to cefepime but had acquired mutations â€" most notably in the wbaP gene, which encodes an enzyme required for the initiation of the synthesis of the polysaccharide capsule and lipopolysaccharide O antigen - that increased their ability to invade and survive within intestinal cells, including cultured human colonocytes. Further, these E. coli mutants exhibited a persister phenotype when exposed to cefepime, allowing for greater survival to pulses of cefepime treatment when compared to the wildtype strain. Our findings highlight a mechanism by which bacteria in the gastrointestinal tract can adapt to antibiotic treatment by increasing their ability to persist during antibiotic treatment and invade intestinal epithelial cells where antibiotic concentrations are substantially reduced.

Determination of antibiotic resistance and biofilm formation in Klebsiella strains isolated from bovine mastitis cases

Mastitis is diseases of dairy cows with a high economic impact. Bovine mastitis is caused by a wide range of bacterial pathogens. As one of the major environmental pathogens Klebsiella ssp. was investigated in this study by some phenotypic characteristics like antibiotic resistance patterns and biofilm formation properties. A number of 483 cows by dairy farms around the Konya were examined by California Mastitis Test (CMT) producing 36 positive in terms of subclinical mastitis. A further 19 samples from clinical mastitic udders were also collected. Samples were inoculated onto Trypticase Soy Agar medium enriched with sheep blood and incubated aerobicaly for 24-48 hours at 37 °C. By morphological, biochemical and cultural charcateristics 14 isolates out of 37 coliform were identified as Klebsiella ssp. The double disc synergy method and Congo Red Agar test were used to perform antibiotic susceptibility and in vitro slime forming properties, respectively. Resistances to the antibiotics Ampicillin, Carbenicillin, Cephotaxime, Chloramphenicol, Erythromycin, Gentamicin, Neomycin, Oxytetracycline, Sulphamethoxazole/Trimpethoprim, Amoxicillin-Clavulanate and Imipenem were 78.5%, 78.5%, 35.7%, 42.8%, 100%, 7%, 7%, 50%, 14%, 21% and 7%, respectively. Three of the total isolets produced biofilm only. This appears to the first report on ESBL producing Klebsiella ssp from subclinical cases of bovine mastitis in Konya, Türkiye. Presently, two numbers of antimicrobial combinations to treat bovine cases are recommended by this work. In conclusion, because of costly challange nature of Klebsiella caused bovine mastitis implemantation of an effective mastitis control program should be used in local farms from Konya.

Extended-Spectrum Beta-Lactamases Producing Enterobacteriaceae in the USA Dairy Cattle Farms and Implications for Public Health

Antimicrobial resistance (AMR) is one of the top global health threats of the 21th century. Recent studies are increasingly reporting the rise in extended-spectrum beta-lactamases producing Enterobacteriaceae (ESBLs-Ent) in dairy cattle and humans in the USA. The causes of the increased prevalence of ESBLs-Ent infections in humans and commensal ESBLs-Ent in dairy cattle farms are mostly unknown. However, the extensive use of beta-lactam antibiotics, especially third-generation cephalosporins (3GCs) in dairy farms and human health, can be implicated as a major driver for the rise in ESBLs-Ent. The rise in ESBLs-Ent, particularly ESBLs-Escherichia coli and ESBLs-Klebsiella species in the USA dairy cattle is not only an animal health issue but also a serious public health concern. The ESBLs-E. coli and -Klebsiella spp. can be transmitted to humans through direct contact with carrier animals or indirectly through the food chain or via the environment. The USA Centers for Disease Control and Prevention reports also showed continuous increase in community-associated human infections caused by ESBLs-Ent. Some studies attributed the elevated prevalence of ESBLs-Ent infections in humans to the frequent use of 3GCs in dairy farms. However, the status of ESBLs-Ent in dairy cattle and their contribution to human infections caused by ESBLs-producing enteric bacteria in the USA is the subject of further study. The aims of this review are to give in-depth insights into the status of ESBL-Ent in the USA dairy farms and its implication for public health and to highlight some critical research gaps that need to be addressed.

A review: Virulence factors of Klebsiella pneumonia as emerging infection on the food chain

Health problems can be caused by consuming foods that have been processed in unsanitary conditions; hence, the study of the impact of contamination on food and its prevention has become critical. The disease caused by Klebsiella pneumoniae in food is increasing significantly every year across the world. The main factors that are essential for the virulence of K. pneumoniae are lipopolysaccharide and polysaccharide capsules. Furthermore, K. pneumoniae is capable of forming biofilms. Capsule polysaccharides, fimbriae types 1 and 3, are crucial virulence factors contributing to biofilm formation in K. pneumoniae. The food contamination by K. pneumoniae may not directly pose a public health risk; however, the presence of K. pneumoniae refers to unhygienic practices in food handling. This article aims to demonstrate that K. pneumoniae should be considered as a potential pathogen that spreads through the food chain and that necessary precautions should be taken in the future.

Identification of a Novel IncHI1B Plasmid in MDR Klebsiella pneumoniae 200 from Swine in China

Multidrug-resistant (MDR) Klebsiella pneumoniae poses a seriously threat to public health. The aim of this study was to better understand the genetic structure of its plasmids and chromosomes. The whole-genome sequence of K. pneumoniae 200 isolated from the liver of a swine with diarrhea in China was determined using PacBio RS II and Illumina MiSeq sequencing. The complete sequences of the chromosomal DNA and the plasmids were analyzed for the presence of resistance genes. The phylogenetic trees revealed that K. pneumoniae 200 displayed the closest relationship to a human-associated K. pneumoniae strain from Thailand. K. pneumoniae 200 contained two plasmids, pYhe2001 and pYhe2002, belonging to the incompatibility groups IncH-HI1B and IncF-FIA. The plasmid pYhe2001 was a novel plasmid containing four types of heavy metal resistance genes and a novel Tn6897 transposon flanked by two copies of IS26 at both ends. Mixed plasmids could be transferred from K. pneumoniae 200 to Escherichia coli DH5α through transformation together. This study reported the first time a novel plasmid pYhe2001 from swine origin K. pneumoniae 200, suggesting that the plasmids may act as reservoirs for various antimicrobial resistance genes and transport multiple resistance genes in K. pneumoniae of both animal and human origin.

Distribution and genetic diversity of multi-drug-resistant Klebsiella pneumoniae at the human–animal–environment interface in Pakistan

Klebsiella pneumoniae is ubiquitous and known to be a notorious pathogen of humans, animals, and plant-based foods. K. pneumoniae is a recognized trafficker of antibiotic resistance genes (ARGs) between and from different ecological niches. A total of 775 samples (n = 775) were collected from September 2017 to August 2019 from humans, animals, and environmental sources by applying the random convenient sampling technique. A total of 120 (15.7%) samples were confirmed as K. pneumoniae. The distribution of K. pneumoniae among humans, the environment, and animals was 17.1, 12.38, and 10%, respectively. Isolates have shown significant resistance against all the subjected antibiotics agents except colistin. ARGs profiling revealed that the highest percentage prevalence (67.5%) of bla_CTX–M was estimated in the isolates, and various carbapenem resistance genes that were found in the study were bla_NDM–1 (43.3%), bla_OXA–48 (38%), and (1.67%) bla_KPC–2. Overall, 21 distinct sequence types (ST) and 13 clonal complexes (CCs) were found through the multi-locus sequence typing (MLST) analysis. Taking together, the distribution of multi-drug resistance (MDR) K. pneumoniae clones in the  community and associated environment is alarming for the health care system of the country. Health policymakers should consider the role of all the integral parts of humans, animals, and the associated environment intently to cope with this serious public and animal health concern.

FastANI, Mash and Dashing equally differentiate between Klebsiella species

Bacteria of the genus Klebsiella are among the most important multi-drug resistant human pathogens, though they have been isolated from a variety of environments. The importance and ubiquity of these organisms call for quick and accurate methods for their classification. Average Nucleotide Identity (ANI) is becoming a standard for species delimitation based on whole genome sequence comparison. However, much faster genome comparison tools have been appearing in the literature. In this study we tested the quality of different approaches for genome-based species delineation against ANI. To this end, we compared 1,189 Klebsiella genomes using measures calculated with Mash, Dashing, and DNA compositional signatures, all of which run in a fraction of the time required to obtain ANI. Receiver Operating Characteristic (ROC) curve analyses showed equal quality in species discrimination for ANI, Mash and Dashing, with Area Under the Curve (AUC) values above 0.99, followed by DNA signatures (AUC: 0.96). Accordingly, groups obtained at optimized cutoffs largely agree with species designation, with ANI, Mash and Dashing producing 15 species-level groups. DNA signatures broke the dataset into more than 30 groups. Testing Mash to map species after adding draft genomes to the dataset also showed excellent results (AUC above 0.99), producing a total of 26 Klebsiella species-level groups. The ecological niches of Klebsiella strains were found to neither be related to species delimitation, nor to protein functional content, suggesting that a single Klebsiella species can have a wide repertoire of ecological functions.

Phenotypic and Genetic Characterization of Klebsiella pneumoniae Isolates from Wild Animals in Central Italy

Despite Klebsiella pneumoniae being widely recognized as a nosocomial pathogen, there is a critical lack in defining its reservoirs and sources of infections. Most studies on risk factors have focused on multidrug-resistant (MDR) isolates and clinically-oriented questions. Over a two-year period, we sampled 131 wild animals including mammal and bird species from three regions of Central Italy. All typical colonies isolated from the analytical portions were confirmed by real-time PCR and identified by MALDI-TOF mass spectrometry (MALDI-TOF MS). All confirmed K. pneumoniae isolates were tested for antimicrobial susceptibility to 29 antimicrobials and subjected to whole genome sequencing. Typical colonies were detected in 17 samples (13%), which were identified as K. pneumoniae (n = 16) and as K. quasipneumoniae (n = 1) by MALDI-TOF MS. The antimicrobial susceptibility profile showed that all the isolates were resistant to β-lactams (ceftobiprole, cloxacillin, cefazolin) and tetracycline; resistance to ertapenem and trimethoprim was observed and nine out of 16 K. pneumoniae isolates (56.2%) were classified as MDR. Genomic characterization allowed the detection of fluoroquinolone resistance-associated efflux pumps, fosfomycin and β-lactamase resistance genes, and virulence genes in the overall dataset. The cluster analysis of two isolates detected from wild boar with available clinical genomes showed the closest similarity. This study highlights the link between humans, domestic animals, and wildlife, showing that the current knowledge on this ecological context is lacking and that the potential health risks are underestimated.

Multicenter Surveillance of Capsular Serotypes, Virulence Genes, and Antimicrobial Susceptibilities of Klebsiella pneumoniae Causing Bacteremia in Taiwan, 2017–2019

We conducted a longitudinal epidemiological surveillance of hypervirulent Klebsiella pneumoniae (hvKP) in Taiwan. Bacteremic KP isolates collected from 16 hospitals in Taiwan between 2017 and 2019 were collected, and the virulent serotypes (K1, K2, K20, K54, and K57), antimicrobial susceptibilities, and virulence genes of these isolates were investigated. During the 3-year period, 1,310 bacteremic KP isolates were collected, of which 27.5% belonged to virulent serotypes, including K1 (n = 162), K2 (n = 74), K57 (n = 56), K54 (n = 41), and K20 (n = 27). K1 was the most prevalent capsular serotype, with an annual prevalence of 11–15%, and was equally distributed across the four geographic areas. The prevalence of K2 declined significantly in 2019. According to wzi-K typing results, 87% of K1 isolates were classified as wzi-1. Among K2 isolates, wzi-72 (55.4%) and wzi-2 (41.9%) were the most common, whereas wzi-206 was the most prevalent (48.2%) among K57 isolates, followed by wzi-77 (25.0%). Wzi-115 accounted for 85.4% of the K54 isolates, whereas wzi-95 accounted for 92.6% of K20 isolates. rmpA was present in 99.4% of K1, 98.6% of K2, 89.3% of K57, 78.0% of K54, and 84.0% of K20 isolates. rmpA2 was present in 100% of K1 and 98.6% of K2 isolates but was only present in 64.3% of K57, 58.5% of K54, and 74.1% of K20 isolates. K1 remains the dominant hvKP serotype and is associated with most virulence genes in Taiwan. Further studies are required to elucidate the significance of other virulent serotypes.

High Prevalence of Klebsiella pneumoniae in European Food Products: a Multicentric Study Comparing Culture and Molecular Detection Methods

The Klebsiella pneumoniae species complex (KpSC) is a leading cause of multidrug-resistant human infections. To better understand the potential contribution of food as a vehicle of KpSC, we conducted a multicentric study to define an optimal culture method for its recovery from food matrices and to characterize food isolates phenotypically and genotypically. Chicken meat (n = 160) and salad (n = 145) samples were collected in five European countries and screened for the presence of KpSC using culture-based and zur-khe intergenic region (ZKIR) quantitative PCR (qPCR) methods. Enrichment using buffered peptone water followed by streaking on Simmons citrate agar with inositol (44°C for 48 h) was defined as the most suitable selective culture method for KpSC recovery. A high prevalence of KpSC was found in chicken meat (60% and 52% by ZKIR qPCR and the culture approach, respectively) and salad (30% and 21%, respectively) samples. Genomic analyses revealed high genetic diversity with the dominance of phylogroups Kp1 (91%) and Kp3 (6%). A total of 82% of isolates presented a natural antimicrobial susceptibility phenotype and genotype, with only four CTX-M-15-producing isolates detected. Notably, identical genotypes were found across samples-same food type and same country (15 cases), different food types and same country (1), and same food type and two countries (1)-suggesting high rates of transmission of KpSC within the food sector. Our study provides a novel isolation strategy for KpSC from food matrices and reinforces the view of food as a potential source of KpSC colonization in humans. IMPORTANCE Bacteria of the Klebsiella pneumoniae species complex (KpSC) are ubiquitous, and K. pneumoniae is a leading cause of antibiotic-resistant infections in humans. Despite the urgent public health threat represented by K. pneumoniae, there is a lack of knowledge of the contribution of food sources to colonization and subsequent infection in humans. This is partly due to the absence of standardized methods for characterizing the presence of KpSC in food matrices. Our multicentric study provides and implements a novel isolation strategy for KpSC from food matrices and shows that KpSC members are highly prevalent in salads and chicken meat, reinforcing the view of food as a potential source of KpSC colonization in humans. Despite the large genetic diversity and the low levels of resistance detected, the occurrence of identical genotypes across samples suggests high rates of transmission of KpSC within the food sector, which need to be further explored to define possible control strategies.

Infectious coryza in a grey crowned crane (Balearica regulorum) recovered from captivity

We report Avibacterium paragallinarum and Klebsiella pneumoniae coinfection in a grey crowned crane (Balearica regulorum). The crane was recovered from illegal captivity and released at a grey crowned crane (GCC) rehabilitation facility located at Akagera National Park in Rwanda. One year after being transferred, the bird presented with clinical signs suggesting a respiratory disease. Those signs included severe dyspnoea with mouth breathing, sneezing and nasal discharge. The crane was put on a 3‐day treatment with antibiotics (ceftiofur 200 mg/ml at 50 mg/kg intramuscularly) and anti‐inflammatory drug (meloxicam, intramuscular injection at a dose of 2 mg/kg), after which the crane seemed to have recovered. A month later, the same crane presented similar clinical signs and was treated with enrofloxacin at 10 mg/kg intramuscularly. Despite the treatment, the crane died 19 h later. At necropsy, adhesive air sacculitis and hydroperitoneum were observed, and a reddish fluid in air sacs and in the abdominal cavity was found. Also, a marked hepatomegaly and splenomegaly were observed. Samples were collected for laboratory examination. Molecular tests done on the tracheal and cloacal swabs revealed A. paragallinarum and K. pneumoniae, respectively. This is the first case of A. paragallinarum and K. pneumoniae coinfection reported in a grey crowned crane. Our study contributes to knowledge on the ecological distribution of both these pathogens in wild birds. It provides an opportunity to investigate further the clinical significance of infectious coryza in Rwanda's wild and domestic birds.

Avibacterium paragallinarum and Klebsiella pneumoniae are the main causes of respiratory infections in domestic bird species. These pathogens are rarely reported in coinfection and never reported in wild birds. While Avibacterium paragallinarum only causes disease in avian species, Klebsiella pneumoniae is zoonotic and causes human infections including pneumonia, bloodstream infections, wound or surgical site infections, and meningitis. Illegal captivity and keeping wildlife as pets could potentially be a source of pathogen spillover events between wildlife, humans, and other livestock species.

Diversity in the Characteristics of Klebsiella pneumoniae ST101 of Human, Environmental, and Animal Origin

Background

Klebsiella pneumoniae ST101 is an emerging high-risk clone which exhibits extensive drug resistance. Bacterial strains residing in multiple hosts show unique signatures related to host adaptation. In this study, we assess the genetic relationship of K. pneumoniae ST101 isolated from hospital samples, the environment, community, and livestock using whole genome sequencing (WGS).

Materials and Methods

We selected ten K. pneumoniae ST101 strains from hospitalized patients in Italy (n = 3) (2014) and Spain (n = 5) (2015–2016) as well as Belgian livestock animals (n = 2) (2017–2018). WGS was performed with 2 × 250 bp paired-end sequencing (Nextera XT) sample preparation kit and MiSeq (Illumina Inc.). Long-read sequencing (Pacbio Sequel I) was used to sequence the two livestock strains and three Italian hospital-associated strains. Furthermore, a public ST101 sequence collection of 586 strains (566 hospital-associated strains, 12 environmental strains, six strains from healthy individuals, one food-associated strain and one pig strain) was obtained. BacPipe and Kleborate were used to conduct genome analysis. ISFinder was used to find IS elements, and PHASTER was utilized to identify prophages. A phylogenetic tree was constructed to illustrate genetic relatedness.

Results

Hospital-associated K. pneumoniae ST101 showed higher resistance scores than non-clinical isolates from healthy individuals, the environment, food and livestock (1.85 ± 0.72 in hospital-associated isolates vs. 1.14 ± 1.13 in non-clinical isolates, p < 0.01). Importantly, the lack of integrative conjugative elements ICEKp bearing iron-scavenging yersiniabactin siderophores (ybt) in livestock-associated strains suggests a lower pathogenicity potential than hospital-associated strains. Mobile genetic elements (MGE) appear to be an important source of diversity in K. pneumoniae ST101 strains from different origins, with a highly stable genome and few recombination events outside the prophage-containing regions. Core genome MLST based analysis revealed a distinct genetic clustering between human and livestock-associated isolates.

Conclusion

The study of K. pneumoniae ST101 hospital-associated and strains from healthy individuals and animals revealed a genetic diversity between these two groups, allowing us to identify the presence of yersiniabactin siderophores in hospital-associated isolates. Resistance and virulence levels in livestock-associated strains were considerably lower than hospital-associated strains, implying that the public health risk remains low. The introduction of an ICEKp into animal strains, on the other hand, might pose a public threat over time.

Detection of Klebsiella Pneumoniae Antibiotic-Resistant Genes: An Impending Source of Multidrug Resistance Dissemination Through Raw Food

This study aimed to find out the prevalence and antimicrobial resistance profile of Klebsiella pneumoniae in raw food items. A total of 261 raw food items, including vegetables, fruits, meat, and milk samples, were collected and processed for isolation of K. pneumoniae. Further antimicrobial susceptibility testing and molecular analysis was done to analyze the drug resistance encoding genes. The prevalence rate of K. pneumoniae was found to be high (38%), and the raw milk samples were predominantly contaminated (19/51), followed by fruits (12/51), meat (11/51), and vegetables (9/51). However, no significant association was observed for the isolation of K. pneumoniae and any particular specimen. Among the isolates, 43% were extended-spectrum β-lactamase producers, 24% were AmpC, and 20% were carbapenemase producers. The highest rates of ESBLs and AmpC were observed in vegetables (cabbage, bell pepper, and spinach) and carbapenemases in raw chicken, fish, and raw meat samples. Notably, bla_CTX-M was the most prevalent, followed by bla_SHV and bla_TEM. Six K. pneumoniae possessed bla_MOX, and five possessed bla_FOX genes. Numerous carbapenemases were identified with a higher proportion of bla_NDM. This study indicates that raw vegetables, fruits, meat, and milk are exposed to contaminants. These findings imply a potential threat that drug-resistant K. pneumoniae pathogens could transmit to humans through raw vegetables, fruits, and meat.

Degradation of antibiotic resistance genes and mobile gene elements in dairy manure anerobic digestion

Antibiotic resistance genes (ARGs) are emerging contaminants causing serious global health concern. Interventions to address this concern include improving our understanding of methods for treating waste material of human and animal origin that are known to harbor ARGs. Anaerobic digestion is a commonly used process for treating dairy manure, and although effective in reducing ARGs, its mechanism of action is not clear. In this study, we used three ARGs to conducted a longitudinal bench scale anaerobic digestion experiment with various temperatures (28, 36, 44, and 52°C) in triplicate using fresh dairy manure for 30 days to evaluate the reduction of gene abundance. Three ARGs and two mobile genetic elements (MGEs) were studied: sulfonamide resistance gene (sulII), tetracycline resistance genes (tetW), macrolide-lincosamide-streptogramin B (MLSB) superfamily resistance genes (ermF), class 1 integrase gene (intI1), and transposase gene (tnpA). Genes were quantified by real-time quantitative PCR. Results show that the thermophilic anaerobic digestion (52°C) significantly reduced (p < 0.05) the absolute abundance of sulII (95%), intI1 (95%), tnpA (77%) and 16S rRNA gene (76%) after 30 days of digestion. A modified Collins–Selleck model was used to fit the decay curve, and results suggest that the gene reduction during the startup phase of anaerobic digestion (first 5 days) was faster than the later stage, and reductions in the first five days were more than 50% for most genes.

Soul of the Jukskei River: The Extent of Bacterial Contamination in the Jukskei River in Gauteng Province, South Africa

River water quality is an important health issue as the water is utilised for drinking, domestic and agricultural use in developing countries. This study aimed to investigate the effect water from a major city has on the water quality of the Jukskei River that daylights in Johannesburg, South Africa. The river water samples were analysed for physio-chemical properties, microbiology, antibiotic resistance of bacterial isolates, genetic markers, and potentially toxic metals. Data analysis revealed increased electrical conductivity, total dissolved solids, and turbidity since 2010. Total Coliform and Escherichia coli detected were above the South African water quality guidelines for domestic, recreational, and irrigation purposes. Additionally, sodium, zinc, nickel, lithium, and lead exceeded the guidelines in domestic, recreational, and irrigation water. Pathogenic strains of E. coli (aEPEC, EHEC, EIEC, and EAEC) were isolated from the water. Various other potentially pathogenic organisms that have been implicated as causes of gastro-intestinal, and a wide range of other diseases, were also detected and demonstrated multiple levels of resistance to antibiotics tested. The results show that the river water is a potential health threat to downstream users. These results will feed into the environmental management action plan for Water for the Future (NGO group).

Environmental Spread of Antibiotic Resistance

Antibiotic resistance represents a global health concern. Soil, water, livestock and plant foods are directly or indirectly exposed to antibiotics due to their agricultural use or contamination. This selective pressure has acted synergistically to bacterial competition in nature to breed antibiotic-resistant (AR) bacteria. Research over the past few decades has focused on the emergence of AR pathogens in food products that can cause disease outbreaks and the spread of antibiotic resistance genes (ARGs), but One Health approaches have lately expanded the focus to include commensal bacteria as ARG donors. Despite the attempts of national and international authorities of developed and developing countries to reduce the over-prescription of antibiotics to humans and the use of antibiotics as livestock growth promoters, the selective flow of antibiotic resistance transmission from the environment to the clinic (and vice-versa) is increasing. This review focuses on the mechanisms of ARG transmission and the hotspots of antibiotic contamination resulting in the subsequent emergence of ARGs. It follows the transmission of ARGs from farm to plant and animal food products and provides examples of the impact of ARG flow to clinical settings. Understudied and emerging antibiotic resistance selection determinants, such as heavy metal and biocide contamination, are also discussed here.

Genome-Based Analysis of Klebsiella spp. Isolates from Animals and Food Products in Germany, 2013-2017

The increase in infections with multidrug-resistant and virulent Klebsiella pneumoniae (K. pneumoniae) strains poses a serious threat to public health. However, environmental reservoirs and routes of transmission for Klebsiella spp. that cause infections in humans and in livestock animals are not well understood. In this study, we aimed to analyze the distribution of antibiotic resistance genes and important virulence determinants (ybt, clb, iro, iuc, rmpA/A2) among 94 Klebsiella spp. isolates from different animal and food sources isolated between 2013 and 2017 in Germany. Antibiotic susceptibility testing was performed, and the genomes were sequenced by Illumina and Nanopore technology. Genetic relationships were assessed by conducting core genome multilocus sequence typing (cgMLST). Kleborate was used to predict resistance and virulence genes; Kaptive was used to derive the capsule types. The results revealed that 72 isolates (76.6%) belonged to the K. pneumoniae sensu lato complex. Within this complex, 44 known sequence types (STs), 18 new STs, and 38 capsule types were identified. Extended-spectrum beta-lactamase (ESBL) genes were detected in 16 isolates (17.0%) and colistin resistance in one (1.1%) K. pneumoniae isolate. Virulence genes were found in 22 K. pneumoniae isolates. Overall, nine (9.6%) and 18 (19.1%) isolates possessed the genes ybt and iuc, respectively. Notably, aerobactin (iuc lineage 3) was only detected in K. pneumoniae isolates from domestic pigs and wild boars. This study provides a snapshot of the genetic diversity of Klebsiella spp. in animals and food products in Germany. The siderophore aerobactin was found to be more prevalent in K. pneumoniae strains isolated from pigs than other sources. Further investigations are needed to evaluate if pigs constitute a reservoir for iuc lineage 3.

Antimicrobial resistance in Klebsiella species from milk specimens submitted for bovine mastitis testing at the Wisconsin Veterinary Diagnostic Laboratory, 2008–2019

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Klebsiella isolates resistant to ceftiofur, cephalothin, or tetracycline did not increase.

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For sulfadimethoxine, the proportion of resistant isolates decreased over time.

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There was no trend toward increasing antimicrobial resistance among isolates.

The purpose of this retrospective study was to describe antimicrobial resistance trends in Klebsiella isolates cultured from milk samples submitted to the Wisconsin Veterinary Diagnostic Laboratory for bovine mastitis testing. In vitro antimicrobial susceptibility testing was conducted in 483 Klebsiella isolates cultured from 63,841 milk samples submitted from January 1, 2008, through December 31, 2019. The Wisconsin Veterinary Diagnostic Laboratory conducted antimicrobial susceptibility testing according to the Clinical and Laboratory Standards Institute by using a broth microdilution panel. Ten antimicrobials were tested in the panel: ampicillin, penicillin, erythromycin, oxacillin + 2% NaCl, pirlimycin, penicillin/novobiocin, tetracycline, ceftiofur, cephalothin, and sulfadimethoxine. Isolates were considered resistant to specific antimicrobials based on minimum inhibitory concentrations described in Clinical and Laboratory Standards Institute guidelines. No guidelines were available for sulfadimethoxine; isolates were categorized as resistant when bacterial growth was not inhibited. The proportion of isolates resistant to ceftiofur, cephalothin, or tetracycline did not increase over time. For sulfadimethoxine, the proportion of resistant isolates decreased over time. These results do not demonstrate a trend toward increasing antimicrobial resistance among Klebsiella isolates. Despite that, antimicrobial resistance should continue to be monitored.

Antibiotic resistance of Escherichia coli and Salmonella spp. strains isolated from healthy poultry farms in the districts of Abidjan and Agnibilékrou (Côte d'Ivoire)

Background and Aim

Antimicrobial resistance (AMR) is a serious challenge to animal and human health worldwide. Therefore, this study aims to determine levels and patterns of AMR of Escherichia coli and Salmonella spp. strains isolated from poultry farms in Côte d'Ivoire.

Materials and Methods

A cross-sectional study was conducted in two districts of Côte d'Ivoire with high poultry production: Abidjan and Agnibilékrou. A total of 231 fecal samples were collected in 124 poultry farms in both districts. Enterobacteria were isolated and tested for susceptibility to 14 antimicrobial agents using the disk-diffusion method.

Results

A total of 212 E. coli and 36 Salmonella strains were isolated. In Abidjan, 139 collected samples generated 101 E. coli and 23 Salmonella strains, whereas in Agnibilékrou, 92 collected samples generated 111 E. coli and 13 Salmonella strains. Variable resistance levels were recorded for the antibiotics tested. The resistance prevalence of E. coli and Salmonella, respectively, was high: Doxycycline (98%/94%), sulfonamide (84%/86%), trimethoprim-sulfamethoxazole (80%/41%), and streptomycin (71%/52%). Average resistance rates were recorded for flumequine (38%/66%), ampicillin (49%/33%), amoxicillin (25%/44%), colistin (26%/2%), chloramphenicol (21%/2%), and gentamicin (4%/47%). The antibiotics least affected by resistance were cefuroxime (4%/5%), ceftriaxone (2%/0.00%), and nitrofurantoin (1%/0.00%).

Conclusion

In this study, it was observed that resistance to important antibiotics is emerging in poultry production in Côte d'Ivoire. Policies promoting the rational use of antibiotics should be implemented to manage antibiotic resistance in animal production.

Characterization and Full Genome Sequence of Novel KPP-5 Lytic Phage against Klebsiella pneumoniae Responsible for Recalcitrant Infection

Klebsiella pneumoniae is a hazardous opportunistic pathogen that is involved in many serious human diseases and is considered to be an important foodborne pathogen found in many food types. Multidrug resistance (MDR) K. pneumoniae strains have recently spread and increased, making bacteriophage therapy an effective alternative to multiple drug-resistant pathogens. As a consequence, this research was conducted to describe the genome and basic biological characteristics of a novel phage capable of lysing MDR K. pneumoniae isolated from food samples in Egypt. The host range revealed that KPP-5 phage had potent lytic activity and was able to infect all selected MDR K. pneumoniae strains from different sources. Electron microscopy images showed that KPP-5 lytic phage was a podovirus morphology. The one-step growth curve exhibited that KPP-5 phage had a relatively short latent period of 25 min, and the burst size was about 236 PFU/infected cells. In addition, KPP-5 phage showed high stability at different temperatures and pH levels. KPP-5 phage has a linear dsDNA genome with a length of 38,245 bp with a GC content of 50.8% and 40 predicted open reading frames (ORFs). Comparative genomics and phylogenetic analyses showed that KPP-5 is most closely associated with the Teetrevirus genus in the Autographviridae family. No tRNA genes have been identified in the KPP-5 phage genome. In addition, phage-borne virulence genes or drug resistance genes were not present, suggesting that KPP-5 could be used safely as a phage biocontrol agent.

An high-throughput sequencing approach to the preliminary analysis of bacterial communities associated with changes in amino acid nitrogen, organic acid and reducing sugar contents during soy sauce fermentation

Soy sauce is a traditional fermented soy food for enhancing the umami taste in Asian cuisines. In this study, 16S rRNA gene throughput sequencing analysis showed the bacterial communities and the changes in soy sauce during fermentation. Weissella, Bacillus and Lactococcus were the most abundant at genus level. The uncultured bacterium Weissella and Lactococcus had relatively high abundance at species level. Alpha diversity analysis indicated the bacterial community diversity increased at fermentation initiation, while decreased as fermentation progressed. Based on beta-diversity analysis, four clusters including cluster I (time point A-F), cluster II (G,H), cluster III (I,J) and cluster IV(K) were distinctly separated, indicating the fermentation time significantly affected bacterial community diversity. Also, close associations were found between the bacterial communities in soy sauce and its amino acid nitrogen, organic acid and reducing sugar contents during fermentation. Therefore, it will provide important information for optimization of the soy sauce production process.

National Safety Survey of Animal-use Commercial Probiotics and Their Spillover Effects From Farm to Humans: An Emerging Threat to Public Health

BACKGROUND

Human-use probiotics have recently been associated with clinical infections and antibiotic resistance transfer, raising public concern over their safety. However, despite their extensive application in aquaculture and animal husbandry, the safety of animal-use probiotics remains poorly described.

METHODS

We evaluated the safety of 92 animal-use probiotics from China. The pattern of spread of pathogens from probiotics and the consequent public health implications were also examined by conducting in-field genomic surveillance at 2 farms.

RESULTS

A total of 123 probiotic Bacillus species isolates were obtained from 92 brands of probiotics, of which 45 isolates were resistant to antibiotics. Notably, 33.7% of probiotic products were contaminated with life-threatening pathogens such as Klebsiella pneumoniae. Genomic surveillance at a chicken farm identified an anthrax toxin-positive Bacillus cereus strain in a probiotic product used as a feed supplement, which was transferred into the groundwater and to a nearby fish farm. Following up retrospective analysis of the surveillance data during 2015-2018 in 3 provinces retrieved 2 B. cereus strains from human with intestinal anthrax symptoms and confirmed the transmission of B. cereus from farm to human. Surveillance of anthrax toxin revealed that cya was detected in 8 of 31 farms.

CONCLUSIONS

This study provides the first national safety survey of animal-use probiotics in China and confirms the spillover effects of probiotics from the farms to human. These results suggest that the large-scale application of pathogen-containing probiotics leads to the transfer of pathogens, with worrisome implications for public health. Good Manufacturing Practice should be implemented during the production of all probiotics.Animal-use probiotic products are frequently contaminated with viable pathogenic bacteria. This study revealed that virulent probiotic organisms and contaminating pathogens were colonized with farm animals and shed into the environment, which facilitated the transfer of pathogens to humans.

Molecular assessment of antimicrobial resistance and virulence in multi drug resistant ESBL-producing Escherichia coli and Klebsiella pneumoniae from food fishes, Assam, India

The present study investigated the prevalence of Extended-Spectrum Beta Lactamase (ESBL) -producing E. coli and K. pneumoniae from the food fishes in retail markets in Assam, India. A total of 54 ESBL-producing E. coli and 12 K. pneumoniae isolates were recovered from 79 fish samples and were analyzed for antimicrobial resistance genes (ARGs) and virulence genes. E. coli isolates were categorized as multi drug resistant with resistance up to 12 different antibiotics with multiple antibiotic resistances (MAR) index ranging from 0.26 to 0.63. In E. coli, 100% resistance to cefotaxime along with 6% resistance to ceftazidime (third-generation cephalosporins) was observed. Moreover, 85% of the E. coli isolates were resistant to cefepime, a fourth-generation cephalosporin. K. pneumoniae showed resistance to 11 different antibiotics with MAR index value ranging from 0.21 to 0.57. All K. pneumoniae isolates showed 100% resistance to cefotaxime, 67% resistance to ceftazidime and 75% resistance to cefepime. Molecular characterization of ARGs revealed the presence of CTX-M group 1(CTX-M-15) in almost all E. coli isolates (98%, n = 53) and 100% in K. pneumoniae. A combination of uniplex and multiplex PCRs revealed fewer ARGs in E. coli isolates, with each isolate carrying 3 to 5 genes (tetA, dfrA1, sul1, sul2, qnrB, qnrS, aac(6')-Ib-cr). Majority of the E. coli were assigned to low-virulence phylogroup B1 and A while 8% of them belonged to pathogenic phylogroup D. 31 unique genetic profiles were identified for E. coli isolates by Pulsed-Field Gel Electrophoresis (PFGE) typing. K. pneumoniae isolates were highly diverse with 11 unique genetic profiles and a substantial ARG profile (bla_TEM, bla_SHV, bla_OXA-1-like, tetA, strA, strB, dfrA1, sul1, sul2, qnrB, qnrS, aac(6')-Ib-cr, oqxA, oqxB). The frequency of ARGs ranged between 4 and 11. All K. pneumoniae isolates belonged to capsular serotype with wzi gene. Virulence gene iutA was prominent in all isolates while ybtS and kfu were confirmed in two isolates. Our findings raise concerns that fishes bought for consumption may serve as potential reservoirs of AMR genes and pose serious threat to public health. The study emphasizes the need for extensive surveillance of resistant strains in aquaculture and related settings, their in-depth analysis of population structure and transmission dynamics.

Efficient inactivation of antibiotic resistant bacteria and antibiotic resistance genes by photo-Fenton process under visible LED light and neutral pH

Antibiotic resistance has been recognized as a major threat to public health worldwide. Inactivation of antibiotic resistant bacteria (ARB) and degradation of antibiotic resistance genes (ARGs) are critical to prevent the spread of antibiotic resistance in the environment. Conventional disinfection processes are effective to inactivate water-borne pathogens, yet they are unable to completely eliminate the antibiotic resistance risk. This study explored the potential of the photo-Fenton process to inactivate ARB, and to degrade both extracellular and intracellular ARGs (e-ARGs and i-ARGs, respectively). Using Escherichia coli DH5α with two plasmid-encoded ARGs (tetA and bla_TEM-1) as a model ARB, a 6.17 log ARB removal was achieved within 30 min of applying photo-Fenton under visible LED and neutral pH conditions. In addition, no ARB regrowth occurred after 48-h, demonstrating that this process is very effective to induce permanent disinfection on ARB. The photo-Fenton process was validated under various water matrices, including ultrapure water (UPW), simulated wastewater (SWW) and phosphate buffer (PBS). The higher inactivation efficiency was observed in SWW as compared to other matrices. The photo-Fenton process also caused a 6.75 to 8.56-log reduction in eARGs based on quantitative real-time PCR of both short- and long amplicons. Atomic force microscopy (AFM) further confirmed that the extracellular DNA was sheared into short DNA fragments, thus eliminating the risk of the transmission of antibiotic resistance. As compared with e-ARGs, a higher dosage of Fenton reagent was required to damage i-ARGs. In addition, the tetA gene was more easily degraded than the bla_TEM-1 gene. Collectively, our results demonstrate the photo-Fenton process is a promising technology for disinfecting water to prevent the spread of antibiotic resistance.

Extraintestinal Foodborne Pathogens

In general, foodborne diseases present themselves with gastrointestinal symptoms caused by bacterial, viral, and parasitic pathogens well established to be foodborne. These pathogens are also associated with extraintestinal clinical manifestations. Recent studies have suggested that Escherichia coli and Klebsiella pneumoniae, which both cause common extraintestinal infections such as urinary tract and bloodstream infections, may also be foodborne. The resolution and separation of these organisms into pathotypes versus commensals by modern genotyping methods have led to the identification of key lineages of these organisms causing outbreaks of extraintestinal infections. These epidemiologic observations suggested common- or point-source exposures, such as contaminated food. Here, we describe the spectrum of extraintestinal illnesses caused by recognized enteric pathogens and then review studies that demonstrate the potential role of extraintestinal pathogenic E. coli (ExPEC) and K. pneumoniae as foodborne pathogens. The impact of global food production and distribution systems on the possible foodborne spread of these pathogens is discussed.

The ZKIR Assay, a Real-Time PCR Method for the Detection of Klebsiella pneumoniae and Closely Related Species in Environmental Samples

The Klebsiella pneumoniae species complex Kp includes human and animal pathogens, some of which are emerging as hypervirulent and/or antibiotic-resistant strains. These pathogens are diverse and classified into seven phylogroups, which may differ in their reservoirs and epidemiology. Proper management of this public health hazard requires a better understanding of Kp ecology and routes of transmission to humans. So far, detection of these microorganisms in complex matrices such as food or the environment has been difficult due to a lack of accurate and sensitive methods. Here, we describe a novel method based on real-time PCR which enables detection of all Kp phylogroups with high sensitivity and specificity. We used this method to detect Kp isolates from environmental samples, and we show based on genomic sequencing that they differ in antimicrobial resistance and virulence gene content from human clinical Kp isolates. The ZKIR PCR assay will enable rapid screening of multiple samples for Kp presence and will thereby facilitate tracking the dispersal patterns of these pathogenic strains across environmental, food, animal and human sources.

Klebsiella pneumoniae is of growing public health concern due to the emergence of strains that are multidrug resistant, virulent, or both. Taxonomically, the K. pneumoniae complex (“Kp”) includes seven phylogroups, with Kp1 (K. pneumoniaesensu stricto) being medically prominent. Kp can be present in environmental sources such as soils and vegetation, which could act as reservoirs of animal and human infections. However, the current lack of screening methods to detect Kp in complex matrices limits research on Kp ecology. Here, we analyzed 1,001 genome sequences and found that existing molecular detection targets lack specificity for Kp. A novel real-time PCR method, the ZKIR (zur-khe intergenic region) assay, was developed and used to detect Kp in 96 environmental samples. The results were compared to a culture-based method using Simmons citrate agar with 1% inositol medium coupled to matrix-assisted laser desorption ionization–time of flight mass spectrometry identification. Whole-genome sequencing of environmental Kp was performed. The ZKIR assay was positive for the 48 tested Kp reference strains, whereas 88 non-Kp strains were negative. The limit of detection of Kp in spiked soil microcosms was 1.5 × 10⁻¹ CFU g⁻¹ after enrichment for 24 h in lysogeny broth supplemented with ampicillin, and it was 1.5 × 10³ to 1.5 × 10⁴ CFU g⁻¹ directly after soil DNA extraction. The ZKIR assay was more sensitive than the culture method. Kp was detected in 43% of environmental samples. Genomic analysis of the isolates revealed a predominance of phylogroups Kp1 (65%) and Kp3 (32%), a high genetic diversity (23 multilocus sequence types), a quasi-absence of antibiotic resistance or virulence genes, and a high frequency (50%) of O-antigen type 3. This study shows that the ZKIR assay is an accurate, specific, and sensitive novel method to detect the presence of Kp in complex matrices and indicates that Kp isolates from environmental samples differ from clinical isolates.

IMPORTANCE The Klebsiella pneumoniae species complex Kp includes human and animal pathogens, some of which are emerging as hypervirulent and/or antibiotic-resistant strains. These pathogens are diverse and classified into seven phylogroups, which may differ in their reservoirs and epidemiology. Proper management of this public health hazard requires a better understanding of Kp ecology and routes of transmission to humans. So far, detection of these microorganisms in complex matrices such as food or the environment has been difficult due to a lack of accurate and sensitive methods. Here, we describe a novel method based on real-time PCR which enables detection of all Kp phylogroups with high sensitivity and specificity. We used this method to detect Kp isolates from environmental samples, and we show based on genomic sequencing that they differ in antimicrobial resistance and virulence gene content from human clinical Kp isolates. The ZKIR PCR assay will enable rapid screening of multiple samples for Kp presence and will thereby facilitate tracking the dispersal patterns of these pathogenic strains across environmental, food, animal and human sources.

Characterization of a Multidrug-Resistant Porcine Klebsiella pneumoniae Sequence Type 11 Strain Coharboring bla KPC-2 and fosA3 on Two Novel Hybrid Plasmids

The global dissemination of carbapenem resistance genes is of great concern. Animals are usually considered a reservoir of resistance genes and an important source of human infection. Although carbapenemase-producing Enterobacteriaceae strains of animal origin have been reported increasingly, bla_KPC-2-positive strains from food-producing animals are still rare. In this study, we first describe the isolation and characterization of a carbapenem-resistant Klebsiella pneumoniae ST11 isolate, strain K15, which is of pig origin and coproduces KPC-2 and FosA3 via two novel hybrid plasmids. Furthermore, our findings highlight that this ST11 Klebsiella pneumoniae strain K15 is most likely of human origin and could be easily transmitted back to humans via direct contact or food intake. In light of our findings, significant attention must be paid to monitoring the prevalence and further evolution of bla_KPC-2-carrying plasmids among the Enterobacteriaceae strains of animal origin.

The occurrence of carbapenemase-producing Enterobacteriaceae (CPE) poses a considerable risk for public health. The gene for Klebsiella pneumoniae carbapenemase-2 (KPC-2) has been reported in many countries worldwide, and KPC-2-producing strains are mainly of human origin. In this study, we identified two novel hybrid plasmids that carry either bla_KPC-2 or the fosfomycin resistance gene fosA3 in the multiresistant K. pneumoniae isolate K15 of swine origin in China. The bla_KPC-2-bearing plasmid pK15-KPC was a fusion derivative of an IncF33:A−:B− incompatibility group (Inc) plasmid and chromosomal sequences of K. pneumoniae (CSKP). A 5-bp direct target sequence duplication (GACTA) was identified at the boundaries of the CSKP, suggesting that the integration might have been due to a transposition event. The bla_KPC-2 gene on pK15-KPC was in a derivative of ΔTn6296-1. The multireplicon fosA3-carrying IncN-IncR plasmid pK15-FOS also showed a mosaic structure, possibly originating from a recombination between an epidemic fosA3-carrying pHN7A8-like plasmid and a pKPC-LK30-like IncR plasmid. Stability tests demonstrated that both novel hybrid plasmids were stably maintained in the original host without antibiotic selection but were lost from the transformants after approximately 200 generations. This is apparently the first description of a porcine sequence type 11 (ST11) K. pneumoniae isolate coproducing KPC-2 and FosA3 via pK15-KPC and pK15-FOS, respectively. The multidrug resistance (MDR) phenotype of this high-risk K. pneumoniae isolate may contribute to its spread and its persistence.

IMPORTANCE The global dissemination of carbapenem resistance genes is of great concern. Animals are usually considered a reservoir of resistance genes and an important source of human infection. Although carbapenemase-producing Enterobacteriaceae strains of animal origin have been reported increasingly, bla_KPC-2-positive strains from food-producing animals are still rare. In this study, we first describe the isolation and characterization of a carbapenem-resistant Klebsiella pneumoniae ST11 isolate, strain K15, which is of pig origin and coproduces KPC-2 and FosA3 via two novel hybrid plasmids. Furthermore, our findings highlight that this ST11 Klebsiella pneumoniae strain K15 is most likely of human origin and could be easily transmitted back to humans via direct contact or food intake. In light of our findings, significant attention must be paid to monitoring the prevalence and further evolution of bla_KPC-2-carrying plasmids among the Enterobacteriaceae strains of animal origin.

High rate of multiresistant Klebsiella pneumoniae from human and animal origin

Purpose

The main objectives of the present study were to detect the antimicrobial susceptibility and molecular characteristics of Klebsiella pneumoniae isolated from different hosts and to investigate the possibility of K. pneumoniae transmission between animals and humans.

Materials and methods

A total of 189 nonduplicate K. pneumoniae isolates were collected from hospitals and four species of animals in Henan Province, China. The disk diffusion method was used for antimicrobial susceptibility testing, and resistance and virulence genes were screened by polymerase chain reaction (PCR). The molecular types were identified through multilocus sequence typing (MLST), and the hypermucoviscous (HMV) phenotype was identified using the “string-forming test”. Pearson’s parameters were used to determine the potential link among the molecular types and resistance and virulence genes of all K. pneumoniae strains.

Results

The resistance rates of the 189 K. pneumoniae isolates against 15 antibiotics ranged from 11.6% to 77.8%. The highest multidrug resistance rate was detected in the pig strains (93.6%), followed by the human strains (90.4%), chicken strains (88.9%), cow strains (52.0%) and sheep strains (50.0%). Forty-eight (25.4%) K. pneumoniae strains presented the HMV phenotype. entB, fimH-1 and mrkD were the most prevalent of the detected virulence genes, and magA and rmpA were the least prevalent genes in all the isolates. The MLST analysis revealed 24 unique sequence types (STs) among from the 189 isolates. ST11, ST235 and ST258 were common STs among the five isolates of host origin. ST258 exhibited significantly positive correlations with blaNDM, magA and the HMV phenotype and a negative correlation with qnrB.

Conclusion

K. pneumoniae strains from different hosts, including humans and animals, have common molecular types and similar phenotypes, and these strains can potentially be transmitted between humans and animals.

Molecular Characterization of a Multidrug-Resistant Klebsiella pneumoniae Strain R46 Isolated from a Rabbit

To investigate the mechanisms of multiple resistance and the horizontal transfer of resistance genes in animal pathogens, we characterized the molecular structures of the resistance gene-related sequences in a multidrug-resistant Klebsiella pneumoniae strain R46 isolated from a rabbit. Molecular cloning was performed to clone the resistance genes, and minimum inhibitory concentrations (MICs) were measured to determine the resistance characteristics of the cloned genes and related strains. A conjugation experiment was conducted to assess the transferability of the resistance plasmids. Sequencing and comparative genomic methods were used to analyze the structures of the resistance gene-related sequences. The K. pneumoniae R46 genome consisted of a chromosome and three resistance plasmids named pR46-27, pR46-42, and pR46-270, respectively. The whole genome encoded 34 antibiotic resistance genes including a newly identified chromosome-encoded florfenicol resistance gene named mdfA2. pR46-270, besides encoding 26 antibiotic resistance genes, carried four clusters of heavy metal resistance genes and several virulence-related genes or gene clusters. The plasmid-encoded resistance genes were mostly associated with mobile genetic elements. The plasmid with the most similarity to the floR gene-harboring plasmid pR46-27 was pCTXM-2271, a plasmid from Escherichia coli. The results of this work demonstrated that the plasmids with multidrug resistance genes were present in animal-derived bacteria and more florfenicol resistance genes such as mdfA2 could be present in bacterial populations. The resistance genes encoded on the plasmids may spread between the bacteria of different species or genera and cause the resistance dissemination.

Draft Genomic Sequence of Multidrug-Resistant Klebsiella pneumoniae B8S35, Isolated from Retail Chicken Skin

Here, we report the draft genome sequence of Klebsiella pneumoniae strain B8S35, isolated from retail chicken skin. It carries genes for resistance to multiple antibiotics, as well as quaternary ammonium compounds used by the food and health care industries.

Here, we report the draft genome sequence of Klebsiella pneumoniae strain B8S35, isolated from retail chicken skin. It carries genes for resistance to multiple antibiotics, as well as quaternary ammonium compounds used by the food and health care industries.

New Bacteriophages against Emerging Lineages ST23 and ST258 of Klebsiella pneumoniae and Efficacy Assessment in Galleria mellonella Larvae

Klebsiella pneumoniae is a bacterial pathogen of high public health importance. Its polysaccharide capsule is highly variable but only a few capsular types are associated with emerging pathogenic sublineages. The aim of this work is to isolate and characterize new lytic bacteriophages and assess their potential to control infections by the ST23 and ST258 K. pneumoniae sublineages using a Galleria mellonella larvae model. Three selected bacteriophages, targeting lineages ST258 (bacteriophages vB_KpnP_KL106-ULIP47 and vB_KpnP_KL106-ULIP54) and ST23 (bacteriophage vB_KpnP_K1-ULIP33), display specificity for capsular types KL106 and K1, respectively. These podoviruses belong to the Autographivirinae subfamily and their genomes are devoid of lysogeny or toxin-associated genes. In a G. mellonella larvae model, a mortality rate of 70% was observed upon infection by K. pneumoniae ST258 and ST23. This number was reduced to 20% upon treatment with bacteriophages at a multiplicity of infection of 10. This work increases the number of characterized bacteriophages infecting K. pneumoniae and provides information regarding genome sequence and efficacy during preclinical phage therapy against two prominent sublineages of this bacterial species.

Spread of the florfenicol resistance floR gene among clinical Klebsiella pneumoniae isolates in China

Background

Florfenicol is a derivative of chloramphenicol that is used only for the treatment of animal diseases. A key resistance gene for florfenicol, floR, can spread among bacteria of the same and different species or genera through horizontal gene transfer. To analyze the potential transmission of resistance genes between animal and human pathogens, we investigated floR in Klebsiella pneumoniae isolates from patient samples. floR in human pathogens may originate from animal pathogens and would reflect the risk to human health of using antimicrobial agents in animals.

Methods

PCR was used to identify floR-positive strains. The floR genes were cloned, and the minimum inhibitory concentrations (MICs) were determined to assess the relative resistance levels of the genes and strains. Sequencing and comparative genomics methods were used to analyze floR gene-related sequence structure as well as the molecular mechanism of resistance dissemination.

Results

Of the strains evaluated, 20.42% (67/328) were resistant to florfenicol, and 86.96% (20/23) of the floR-positive strains demonstrated high resistance to florfenicol with MICs ≥512 μg/mL. Conjugation experiments showed that transferrable plasmids carried the floR gene in three isolates. Sequencing analysis of a plasmid approximately 125 kb in size (pKP18-125) indicated that the floR gene was flanked by multiple copies of mobile genetic elements. Comparative genomics analysis of a 9-kb transposon-like fragment of pKP18-125 showed that an approximately 2-kb sequence encoding lysR-floR-virD2 was conserved in the majority (79.01%, 83/105) of floR sequences collected from NCBI nucleotide database. Interestingly, the most similar sequence was a 7-kb fragment of plasmid pEC012 from an Escherichia coli strain isolated from a chicken.

Conclusions

Identified on a transferable plasmid in the human pathogen K. pneumoniae, the floR gene may be disseminated through horizontal gene transfer from animal pathogens. Studies on the molecular mechanism of resistance gene dissemination in different bacterial species of animal origin could provide useful information for preventing or controlling the spread of resistance between animal and human pathogens.

Prevalence and risk factors for faecal carriage of Extended Spectrum β-lactamase producing Enterobacteriaceae among food handlers in lower basic schools in West Coast Region of The Gambia

BACKGROUND

The isolation of Extended spectrum βlactamase (ESBLs) producing Enterobacteriaceae among food handlers and their implication as sources of food borne outbreaks are a public health concern. This study seeks to investigate the prevalence of faecal carriage of these bacteria among food handlers in the West Coast Region of The Gambia.

METHOD

This study enrolled 600 participants from 60 Lower Basic Schools in West Coast Region of the country. Stool samples collected from the participants were presumptively screened for the ESBLs producing Enterobacteriaceae, using Drigalski agar, supplemented with 2mg/L cefotaxime. The bacterial colonies that grew on each Drigalski agar were tested for ESBL production by the double disk synergy test as recommended by Clinical and Laboratory Standard Institute (CLSI-2015). The confirmatory analysis for ESBL was determined as the zone of inhibition of cefotaxime and/or ceftazidime to ≥5mm from that of cefotaxime /clavulanicacid and/or ceftazidime/clavulanic acid. The presumptive screening of isolates for AmpC phenotypes was done by testing the organism against cefoxitin. The prevalence of the ESBL carriage was presented in percentages. The association of risk factors to the faecal carriage of ESBLs producing Enterobacteriaceae was performed by Pearson Chi-squared and Fishers Exact at (p ≤ 0.05).

RESULT

The prevalence of faecal carriage ESBL producing Enterobacteriaceae among food handlers was 5.0% (28/565). We found50% (14/28) and3.57% (1/28) ESBL producing bacteria were presumptive AmpC and carbapenemase resistance phenotype. Themost abundant ESBL producing Enterobacteriaceae were Klebsiella spp 32.1% (9/28) and Escherichia spp 28.6% (8/28). The use of antibiotics in the last 3 months was found to be significantly associated (P = 0.012) with the faecal carriage of ESBLs producing Enterobacteriaceae.

CONCLUSION

The prevalence of faecal carriage of ESBLs producing Enterobacteriaceae among food handlers in the Gambia is low. The history to use of the antibiotics in the last three months was found to be significantly associated with this prevalence. Therefore, the institution of a robust antimicrobial surveillance and treatment of patients with such infections are necessary to curb the spread of these multidrug resistant bacteria in the country. Rational prescription and usage of the antibiotics especially cephalosporin should be advocated both in public and private health facilities.

Extended-spectrum β-lactamases producing multidrug resistance Escherichia coli, Salmonella and Klebsiella pneumoniae in pig population of Assam and Meghalaya, India

Aim

The present study was conducted to record the prevalence of extended spectrum β-lactamases (ESBLs) producing Escherichia coli, Salmonella spp., and Klebsiella pneumoniae from pig population of Assam and Meghalaya and to record the ability of the resistant bacteria to transfer the resistance genes horizontally.

Materials and Methods

Fecal samples (n=228), collected from pigs of Assam (n=99) and Meghalaya (n=129), were processed for isolation and identification of E. coli and Salmonella spp. All the isolates were tested for ESBLs production by double disc synergy test (DDST) followed by screening for ESBLs producing genes (bla_TEM, bla_SHV, bla_CTX-M, and bla_CMY) by polymerase chain reaction (PCR). Possible transfer of resistance encoding genes between enteric bacterial species was carried out by in vitro and in vivo horizontal gene transfer (HGT) method.

Results

A total of 897 enteric bacteria (867 E. coli and 30 Salmonella) were isolated and identified. Altogether 25.41% isolates were confirmed as ESBL producers by DDST method. Majority of the isolates were E. coli followed by Salmonella. By PCR, 9.03% isolates were found positive for at least one of the target resistance genes. bla_SHV was absent in all the isolates. bla_CMY was the most prevalent gene. All the E. coli isolates from Assam were negative for bla_TEM. A total of 2.76% isolates were positive for bla_TEM + bla_CMY. On the other hand, 0.67% isolates were positive for bla_CTX-M + bla_CMY genes. Only 0.33% isolates carried all the three genes. Altogether, 4.68% bacteria carried the resistance encoding genes in their plasmids. bla_TEM gene could be successfully transferred from Salmonella (donor) to E. coli (recipient) by in vitro (5.5-5.7×10^-5) and in vivo (6.5×10^-5 to 8.8×10^-4) methods. In vivo method was more effective than in vitro in the transfer of resistance genes.

Conclusion

The pig population of Assam and Meghalaya are carrying multidrug resistance and ESBLs producing E. coli and Salmonella. The isolates are also capable to transfer their resistance trait to other bacterial species by HGT. The present finding could be considered as a serious public health concern as similar trait can also be transmitted to the human commensal bacteria as well as pathogens.

Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria

Klebsiella pneumoniae is an opportunistic bacterial pathogen known for its high frequency and diversity of antimicrobial resistance (AMR) genes. In addition to being a significant clinical problem in its own right, K. pneumoniae is the species within which several new AMR genes were first discovered before spreading to other pathogens (e.g. carbapenem-resistance genes KPC, OXA-48 and NDM-1). Whilst K. pneumoniae's contribution to the overall AMR crisis is impossible to quantify, current evidence suggests it has a wider ecological distribution, significantly more varied DNA composition, greater AMR gene diversity and a higher plasmid burden than other Gram negative opportunists. Hence we propose it plays a key role in disseminating AMR genes from environmental microbes to clinically important pathogens.

Phenotypic and Genotypic Characterization of Klebsiella pneumoniae Isolated From Retail Foods in China

Klebsiella pneumoniae is not only a major hospital-acquired pathogen but also an important food-borne pathogen that can cause septicaemia, liver abscesses, and diarrhea in humans. The phenotypic and genotypic characteristics of K. pneumoniae in retail foods have not been thoroughly investigated in China. The objective of this study was to characterize K. pneumoniae isolates through biotyping, serotyping, determination of virulence factors, antibiotic resistance testing, enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR), and (GTG)₅-PCR molecular typing. From May 2013 to April 2014, a total of 61 K. pneumoniae isolates were collected from retail foods in China. Using API 20E test strips, five different biotype profiles were identified among these isolates. The majority of isolates belonged to biochemical profile “5215773” (50 isolates, 80.6%). The capsular serotypes of the 61 K. pneumoniae isolates and one reference strain were determined by PCR. Of the seven capsular serotypes tested, four different capsular serotypes were identified. Serotypes K1, K20, K57, and K2 were detected in two, three, two, and one isolates, respectively. Serotypes K3, K5, and K54 were not detected. The presence of 11 virulence genes was assessed by PCR. The most common virulence genes were fimH (85.5%), ureA (79.0%), wabG (77.4%), uge (56.5%), and kfuBC (29.0%). ERIC-PCR and (GTG)₅-PCR molecular typing indicated high genetic diversity among K. pneumoniae isolates. We identified 60 different ERIC patterns and 56 distinct (GTG)₅ patterns. Genotypic results indicated that isolates carrying similar virulence factors were generally genetically related. Some isolates from the same geographic area have a closer relationship. The isolates showed high levels of resistance to ampicillin (51/62, 82.2%). Resistance to streptomycin (11/62, 17.7%) and piperacillin (10/62, 16.1%) was also common. The presence of virulent and antibiotic-resistant K. pneumoniae in foods poses a potential health hazard for consumers. Our findings highlight the importance of surveillance of K. pneumoniae in foods.

Application of high-throughput pyrosequencing in the analysis of microbiota of food commodities procured from small and large retail outlets in a U.S. metropolitan area - A pilot study

With the advent of high-throughput sequencing technologies, it is possible to comprehensively analyze the microbial community of foods without culturing them in the laboratory. The estimation of all microbes inhabiting a food commodity (food microbiota) therefore may shed light on the microbial quality and safety of foods. In this study, we utilized high-throughput pyrosequencing of 16S rRNA genes as well as traditional microbiological methods to evaluate the bacterial diversity and the predicted metabolic pathways associated with the bacterial communities of selected foods (romaine lettuce, cabbage, deli meat, and chicken legs, total 200 samples) procured from small and large retail outlets located in Memphis-Shelby County, Tennessee, USA. For high-throughput sequencing, microbial genomic DNA was directly extracted from the food products and subjected to genetic sequencing. Aerobic plate count of all food samples was also performed. Foods from small stores (such as corner stores) were found to contain higher bacterial counts as compared to large stores (such as supermarkets). High-throughput pyrosequencing in tandem with bioinformatics analyses revealed a comprehensive picture of the bacterial ecology of foods at different taxonomic levels. Firmicutes and Proteobacteria were the most abundant phyla across all products. At the genus level, Enterobacter and Pantoea in vegetables, and Bacillus and Aeromonas in animal products were found to be the most abundant. The bacterial predicted metabolic pathways such as inosine-5'-phosphate biosynthesis I, methylglyoxal (MG) degradation pathways, urea cycle, dTDP-l-rhamnose biosynthesis I, and mevalonate pathway I differed in foods procured from small stores as compared to large groceries or supermarkets. The results from this study revealed that the bacterial ecology (both in terms of numbers and types of bacteria) of food commodities might differ based on the vending outlet type (large vs. small) of retail stores. The overall estimation bacterial communities in foods by high-throughput sequencing method may be useful to identify potential taxa responsible for food spoilage. Moreover, the data from pyrosequencing of 16S rRNA genes can also be applied to infer major metabolic pathways in bacteria inhabiting different foods. This may reflect the role of these pathways in food-bacteria interaction and adaptation.